A method is disclosed for determining repeatable runout (RRO) cancellation values in a disk drive having a head disk assembly (HDA) and a sampled servo controller. The HDA includes a disk having distributed position information in servo wedges, a rotary actuator carrying a head that periodically reads the position information, and a voice coil motor circuit that responds to a control effort signal. The servo controller periodically adjusts the control effort signal during a track-following operation. In the method, the position information related to a predetermined track is read during track following for more than one disk rotation. The position information is averaged for each servo wedge obtained during the disk rotations. The averaged servo position values are filtered with a filter for compensating effects of the sampled servo controller, which tend to distort the averaged servo position values, to generate the RRO cancellation values for the predetermined track.